A CMOS image sensor and a manufacturing method thereof, wherein the gates of several transistors of the CMOS image sensor are formed in an active region defined by an isolation region for a unit pixel of the CMOS image sensor, and a passivation layer composed of insulating layer is formed on the semiconductor substrate. Impurities are ion-implanted into the active region to form one or more diffusion regions of a photo diode of the CMOS image sensor, wherein the passivation layer prevents a boundary portion of the active region from being ion-implanted. Thus, damages by ion implantation at the boundary portion between the diffusion region for the photo diode and the isolation region are prevented, and the dark current of the CMOS image sensor is reduced.